Germination in oleaginous tree Caryocar brasiliense is controlled by complex interactions between pyrene components, contributing to the reproductive success of the species in the seasonal environment of the Cerrado biome. Caryocar brasiliense is an arboreal species widely distributed in the highly seasonal Cerrado (neotropical savanna) biome. The oleaginous fruits of this species are important to the local fauna and as a source of income for traditional human populations. As the diaspores have peculiar structures and pronounced dormancy, we sought to examine the interactions between the morphoanatomy of the pyrene (the seed enveloped by the endocarp) and physiological aspects of germination. We describe here the morphology of the pyrene, the anatomy, histochemistry, and ultrastructure of the seed during the germination process, and evaluate the effect of gibberellic acid (GA3) on the germination of isolated seeds or those still contained within the endocarp. The hard and aculeate endocarp protects the embryo and retards water absorption—thereby controlling germination under natural conditions. The seed coat is thin, unlignified, and rich in phenolic compounds. The embryo is hypocotyledonary, has differentiated vascular bundles, and abundant proteic and lipidc reserves. The physiological dormancy of this species is related to the low growth potential of its embryo and mechanical restraints imposed by the endocarp. Germination is associated with hypocotyl growth through cell expansion (stimulated by GA3)—which promotes the cracking of the endocarp, and thus allows radicle and plumule protrusion. The anatomical characteristics and physiological dormancy of C. brasiliense pyrenes restrict germination to the most propitious occasions and favor the establishment of seedlings in Cerrado environments.